\HeaderA{ParameterList-class}{Class "ParameterList" - List to store all the parameters}{ParameterList.Rdash.class}
\aliasA{show,ParameterList-method}{ParameterList-class}{show,ParameterList.Rdash.method}
\keyword{classes}{ParameterList-class}
\begin{Description}\relax
A simple list-based class for storing all the model parameters of a 
batch of microarray.
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("ParameterList", parameter)} 
where parameter is a list. In the CALIB package, ParameterList objects are 
normally generated by function \code{\LinkA{estimateParameter}{estimateParameter}}.
\end{Section}
\begin{Section}{List Components}
Objects should contain the following list components:
\describe{
\item[\code{MuS}:] Spot parameter. Mean of spot capacity.

\item[\code{Ka}:] Hybridization constant.

\item[\code{P1}:] Respective slope of the linear dye saturation function. It is
different for different dyes.

\item[\code{P2}:] Respective intercept of the linear dye saturation function.
It is different for different dyes

\item[\code{SigmaA}:] Standard deviation of additive error. It is different
for different dyes.

\item[\code{SigmaM}:] Standard deviation of multiplicative error.

\item[\code{SigmaS}:] Spot parameter. Standard deviation of spot capacity.

\item[\code{SpotError}:] numeric matrix containing spot error of all external
control spikes on arrays

\item[\code{Method}:] boolean values indicating the way to calculate the measured 
intensities. It contains two subfields which are both logical value: BC and 
Area. BC indicates whether background corrected measured intensities are used.
Area indicates whether spot area is used to calculate measured intensities. 

\item[\code{ErrorModel}:] a character to represent the distribution of spot capacity.
"L" means spot capacity follows \code{log normal} distribution. "N" means spot 
capacity follows \code{normal} distribution.

\item[\code{genes}:] data.frame containing information on spikes spotted on the arrays.
Should include a character column Name containing names for all the spikes.
}
See reference for more detailed explaination for these list components.
\end{Section}
\begin{Section}{Extends}
Class \code{"list"}, from data part.
Class \code{"vector"}, by class \code{"list"}.
\end{Section}
\begin{Section}{Methods}
This class inherits directly from class List. However since it represents the parameters 
of the calibration model for arrays, it makes on sense to run functions like \code{\LinkA{dim}{dim}}, 
\code{\LinkA{dimnames}{dimnames}},or \code{\LinkA{merge}{merge}} on this class. 
Therefore, only some operations appropriate for list will work on objects of this class. 
ParameterList objects can be \code{\LinkA{cbind}{cbind}} and \code{\LinkA{show}{show}}
in a compact way.

ParameterList objects are used on functions such as \code{\LinkA{normalizeData}{normalizeData}}
or on some other data visualization functions like \code{\LinkA{plotSpikeHI}{plotSpikeHI}}
in the CALIB package.
\end{Section}
\begin{Author}\relax
Hui Zhao
\end{Author}
\begin{References}\relax
Engelen, K., Naudts, B., DeMoor, B., Marchal, K. (2006) 
A calibration method for estimating absolute expression levels from 
microarray data. Bioinformatics  22: 1251-1258.
\end{References}

